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Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YW0 PDB entry 1YW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1.0 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.544 α = 66.97 b = 132.121 β = 85.06 c = 139.95 γ = 89.89
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.21 50 95.8 0.074 0.074 10.7 2.1 224640 224640
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.29 80.5 0.974 2 18873
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YW0 2.4 50.12 170159 170159 8503 93.5 0.21 0.21 0.21 0.1628 0.27 0.235 RANDOM 45.446
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.62 -0.06 -1.34 0.32 0.27 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_3_deg 18.632 r_dihedral_angle_4_deg 18.406 r_scangle_it 7.762 r_scbond_it 6.338 r_mcangle_it 5.842 r_dihedral_angle_1_deg 5.392 r_mcbond_it 4.168 r_angle_refined_deg 1.487 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_3_deg 18.632 r_dihedral_angle_4_deg 18.406 r_scangle_it 7.762 r_scbond_it 6.338 r_mcangle_it 5.842 r_dihedral_angle_1_deg 5.392 r_mcbond_it 4.168 r_angle_refined_deg 1.487 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.296 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.219 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34146 Nucleic Acid Atoms Solvent Atoms 1543 Heterogen Atoms 688
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction CNS phasing